Abstract: In the early modern Japan，the fundamental purpose of the Japanese identity system，which was founded forcibly through politics，was to guarantee the benefits of samurai，lord and Tokugawa Bakufu. But the development of commodity economy resulted in the pauperization of samurai and the rise of wealthy farmers and merchants. This reversal of the economic strength led to the wavering of the Japanese identity system in the early modern Japan. And the priority of samurai could hardly be guaranteed due to the lack of the support of economy. Meanwhile，the lower level warriors gradually became consistent with the wealthy farmers and merchants in the economic interests and the ideology，so they made an alliance with the wealthy farmers and merchants under the historical background of the national crisis in the late Edo Period，which eventually became the important strength to overthrow Tokugawa Bakufu.

Key words: identity system, social structure, commodity economy, the pauperization of samurai, wealthy farmers and merchants